Geothermobacter hydrogeniphilus sp. nov., a mesophilic, iron(III)-reducing bacterium from seafloor/subseafloor environments in the Pacific Ocean, and emended description of the genus Geothermobacter.

A novel mesophilic, anaerobic, mixotrophic bacterium, with designated strains EPR-MT and HR-1, was isolated from a semi-extinct hydrothermal vent at the East Pacific Rise and from an Fe-mat at Lo'ihi Seamount, respectively. The cells were Gram-negative, pleomorphic rods of about 2.0 µm in length and 0.5 µm in width. Strain EPR-MT grew between 25 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l-1 NaCl (optimum, 15-20 g l-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Strain HR-1 grew between 20 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l-1 NaCl (optimum, 15-25 g l-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Shortest generation times with H2 as the primary electron donor, CO2 as the carbon source and ferric citrate as terminal electron acceptor were 6.7 and 5.5 h for EPR-MT and HR-1, respectively. Fe(OH)3, MnO2, AsO4 3-, SO4 2-, SeO4 2-, S2O3 2-, S0 and NO3 - were also used as terminal electron acceptors. Acetate, yeast extract, formate, lactate, tryptone and Casamino acids also served as both electron donors and carbon sources. G+C content of the genomic DNA was 59.4 mol% for strain EPR-MT and 59.2 mol% for strain HR-1. Phylogenetic and phylogenomic analyses indicated that both strains were closely related to each other and to Geothermobacter ehrlichii, within the class δ-Proteobacteria (now within the class Desulfuromonadia). Based on phylogenetic and phylogenomic analyses in addition to physiological and biochemical characteristics, both strains were found to represent a novel species within the genus Geothermobacter, for which the name Geothermobacter hydrogeniphilus sp. nov. is proposed. Geothermobacter hydrogeniphilus is represented by type strain EPR-MT (=JCM 32109T=KCTC 15831T=ATCC TSD-173T) and strain HR-1 (=JCM 32110=KCTC 15832).

Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas.

Three bacterial strains, designated Red330T, Red736T and Red745T, were isolated from forest and paddy soils in Japan. Strains Red330T, Red736T and Red745T are flagella-harbouring and strictly anaerobic bacteria forming red colonies. A 16S rRNA gene sequence-based phylogenetic tree showed that all three strains were located in a cluster, including the type strains of Geomonas species, which were recently separated from the genus Geobacter within the family Geobacteraceae. Similarities of the 16S rRNA gene sequences among the three strains and Geomonas oryzae S43T, the type species of the genus Geomonas, were 96.3-98.5 %. The genome-related indexes, average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity, among the three strains and G. oryzae S43T were 74.7-86.8 %, 21.2-33.3 % and 70.4-89.8 %, respectively, which were lower than the species delineation thresholds. Regarding the phylogenetic relationships based on genome sequences, the three strains clustered with the type strains of Geomonas species, which were independent from the type strains of Geobacter species. The distinguishableness of the three isolated strains was supported by physiological and chemotaxonomic properties, with the profile of availability of electron donors and cellular fatty acids composition being particularly different among them. Based on genetic, phylogenetic and phenotypic properties, the three isolates represent three novel independent species in the genus Geomonas, for which the names Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov. are proposed. The type strains are Red330T (=NBRC 114028T=MCCC 1K03949T), Red736T (=NBRC 114029T=MCCC 1K03950T) and Red745T (=NBRC 114030T=MCCC 1K03951T), respectively.

Desulfomarina profundi gen. nov., sp. nov., a novel mesophilic, hydrogen-oxidizing, sulphate-reducing chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney.

A novel mesophilic, strictly anaerobic, chemolithoautotrophic sulphate-reducing bacterium, designated strain KT2T, was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc. Strain KT2T grew at 25-40 °C (optimum 35 °C) and pH 5.5-7.0 (optimum 6.6) in the presence of 25-45 g l-1 NaCl (optimum 30 g l-1). Growth occurred with molecular hydrogen as the electron donor and sulphate, thiosulphate, and sulphite as the electron acceptors. The isolate utilized CO2 as the sole carbon source for chemolithoautotrophic growth on H2. Glycerol, succinate, fumarate, malate, glutamate, or casamino acids could serve as an alternative electron donor in the presence of CO2. Malate, citrate, glutamate, and casamino acids were used as fermentative substrates for weak growth. The G+C content of genomic DNA was 46.1 %. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain KT2T is a member of the family Desulfobulbaceae, showing a sequence similarity of 94.3 % with Desulforhopalus singaporensis. Phylogenomic analysis based on concatenated 156 single-copy marker genes confirmed the same topology as the 16S rRNA gene phylogeny. The ANI and AAI values between strain KT2T and related genera of the family Desulfobulbaceae were 65.6-68.6 % and 53.1-62.9 %. Based on the genomic, molecular, and physiological characteristics, strain KT2T represents a novel genus and species within the family Desulfobulbaceae, for which the name Desulfomarina profundi gen. nov., sp. nov. is proposed, with KT2T (=JCM 34118T = DSM 111364T) as the type strain.

"Candidatus Desulfobulbus rimicarensis," an Uncultivated Deltaproteobacterial Epibiont from the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata.

The deep-sea hydrothermal vent shrimp Rimicaris exoculata largely depends on a dense epibiotic chemoautotrophic bacterial community within its enlarged cephalothoracic chamber. However, our understanding of shrimp-bacterium interactions is limited. In this report, we focused on the deltaproteobacterial epibiont of R. exoculata from the relatively unexplored South Mid-Atlantic Ridge. A nearly complete genome of a Deltaproteobacteria epibiont was binned from the assembled metagenome. Whole-genome phylogenetic analysis reveals that it is affiliated with the genus Desulfobulbus, representing a potential novel species for which the name "Candidatus Desulfobulbus rimicarensis" is proposed. Genomic and transcriptomic analyses reveal that this bacterium utilizes the Wood-Ljungdahl pathway for carbon assimilation and harvests energy via sulfur disproportionation, which is significantly different from other shrimp epibionts. Additionally, this epibiont has putative nitrogen fixation activity, but it is extremely active in directly taking up ammonia and urea from the host or vent environments. Moreover, the epibiont could be distinguished from its free-living relatives by various features, such as the lack of chemotaxis and motility traits, a dramatic reduction in biosynthesis genes for capsular and extracellular polysaccharides, enrichment of genes required for carbon fixation and sulfur metabolism, and resistance to environmental toxins. Our study highlights the unique role and symbiotic adaptation of Deltaproteobacteria in deep-sea hydrothermal vent shrimps.IMPORTANCE The shrimp Rimicaris exoculata represents the dominant faunal biomass at many deep-sea hydrothermal vent ecosystems along the Mid-Atlantic Ridge. This organism harbors dense bacterial epibiont communities in its enlarged cephalothoracic chamber that play an important nutritional role. Deltaproteobacteria are ubiquitous in epibiotic communities of R. exoculata, and their functional roles as epibionts are based solely on the presence of functional genes. Here, we describe "Candidatus Desulfobulbus rimicarensis," an uncultivated deltaproteobacterial epibiont. Compared to campylobacterial and gammaproteobacterial epibionts of R. exoculata, this bacterium possessed unique metabolic pathways, such as the Wood-Ljungdahl pathway, as well as sulfur disproportionation and nitrogen fixation pathways. Furthermore, this epibiont can be distinguished from closely related free-living Desulfobulbus strains by its reduced genetic content and potential loss of functions, suggesting unique adaptations to the shrimp host. This study is a genomic and transcriptomic analysis of a deltaproteobacterial epibiont and largely expands the understanding of its metabolism and adaptation to the R. exoculata host.

Desulfobotulus mexicanus sp. nov., a novel sulfate-reducing bacterium isolated from the sediment of an alkaline crater lake in Mexico.

A novel Gram-negative, non-spore-forming, vibrio-shaped, anaerobic, alkaliphilic, sulfate-reducing bacterium, designated strain PAR22NT, was isolated from sediment samples collected at an alkaline crater lake in Guanajuato (Mexico). Strain PAR22NT grew at temperatures between 15 and 37 °C (optimum, 32 °C), at pH between pH 8.3 and 10.1 (optimum, pH 9.0-9.6), and in the presence of NaCl up to 10 %. Pyruvate, 2-methylbutyrate and fatty acids (4-18 carbon atoms) were used as electron donors in the presence of sulfate as a terminal electron acceptor and were incompletely oxidized to acetate and CO2. Besides sulfate, both sulfite and elemental sulfur were also used as terminal electron acceptors and were reduced to sulfide. The predominant fatty acids were summed feature 10 (C18 : 1 ω7c and/or C18 : 1 ω9t and/or C18 : 1 ω12t), C18 : 1 ω9c and C16 : 0. The genome size of strain PAR22NT was 3.8 Mb including 3391 predicted genes. The genomic DNA G+C content was 49.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that it belongs to the genus Desulfobotulus within the class Deltaproteobacteria. Its closest phylogenetic relatives are Desulfobotulus alkaliphilus (98.4 % similarity) and Desulfobotulus sapovorans (97.9 % similarity). Based on phylogenetic, phenotypic and chemotaxonomic characteristics, we propose that the isolate represents a novel species of the genus Desulfobotulus with the name Desulfobotulus mexicanus sp. nov. The type strain is PAR22NT (=DSM 105758T=JCM 32146T).

Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau.

Here we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4 cm) of five samples collected in cores in water depths ranging from 2456 to 2728 m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaproteobacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.

Identification of sulfate-reducing and methanogenic microbial taxa in anaerobic bioreactors from industrial wastewater treatment plants using next-generation sequencing and gene clone library analyses.

An understanding of microbial communities present in anaerobic bioreactors can strongly facilitate the development of approaches to control undesirable microorganisms, such as sulfate-reducing bacteria (SRB), in the system. In this study, overall microbial communities present in anaerobic bioreactors from seven industrial wastewater treatment plants (including food, pulp and paper industries) were investigated using 16S rRNA gene amplicon sequencing (MiSeq, Illumina). The dominant methanogens identified in the anaerobic bioreactors treating industrial wastewater were Methanobacterium and Methanosaeta; Methanospirillum was a predominant methanogen in the anaerobic sludge digester. Hydrogenotrophic and acetoclastic methanogens were detected at similar relative abundances in the anaerobic covered lagoons treating starch wastewater, whereas hydrogenotrophic methanogens were the predominant methanogens present in the sludge digester. SRB communities were further investigated using dsrB gene clone libraries. The results indicated the presence of SRB, such as uncultured Desulfobulbus sp., Syntrophobacter fumaroxidans, Syntrophorhabdus sp. PtaB.Bin027, and Desulfovibrio fructosivarans JJ. Incomplete-oxidizing SRB were the predominant SRB in all of the anaerobic bioreactors treating wastewater. In contrast, similar relative abundances of complete and incomplete-oxidizing SRB were observed in the sludge digester. The results of this study can further facilitate the development of SRB-controlling strategies to improve the efficiency of wastewater treatment.

Lujinxingia litoralis gen. nov., sp. nov. and Lujinxingia sediminis sp. nov., two new representatives in the order Bradymonadales.

In this study, two bacterial strains designated B210T and SEH01T, isolated from coastal sediment sampled in Weihai, PR China, were characterized using a polyphasic approach. Strains were Gram-stain-negative, facultative anaerobic, rod-shaped and motile. According to the results of phylogenetic analyses based on their 16S rRNA genes, these two strains should be classified under the order Bradymonadales and they both show <90 % sequence similarities with Bradymonas sediminis FA350T. Moreover, strain B210T showed 98.6 % sequence similarity to strain SEH01T. Genomic characteristics including average nucleotide identity and in silico DNA-DNA hybridization values clearly separated strain B210T from strain SEH01T. The sole quinone of these two strains was menaquinone MK-7, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid. Iso-C15 : 0 was the major fatty acid in both strains B210T and SEH01T, and iso-C14 : 0 3-OH was also a major fatty acid for strain SEH01T. Based on the polyphasic analysis, these two strains represent two novel species of a new genus within the family Bradymonadaceae. Consequently, the novel genus Lujinxingia gen. nov. is proposed, containing two new species Lujinxingia litoralis gen. nov. sp. nov. and Lujinxingia sediminis sp. nov., with strain B210T (=KCTC 42951T=CGMCC 1.16770T) and strain SEH01T (=KCTC 42950T=DSM 101859T) as the type strains, respectively.

Is marine sediment the source of microbes associated with accelerated low water corrosion?

Accelerated low water corrosion (ALWC) is a form of microbiologically influenced corrosion (MIC) associated with the degradation of marine structures around the low tide water level. A better understanding of the role of microbes in this degradation and the source of these microbes is required to improve the prediction and mitigation of the costly failures occurring due to ALWC. The microbial communities present in a sediment sample and on an ALWC tubercle on adjacent steel sheet piling from a tidal estuary were studied using culture-based isolation and metabarcoding. A total of 43 pure cultures were isolated from the sediment using a variety of culture conditions. Phylogenetic analysis of their 16S rRNA genes placed them in the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria (Alphaproteobacteria and Gammaproteobacteria). 16S rRNA gene metabarcoding of the sediment and tubercle revealed similar microbial groups at varying relative abundances. No Deltaproteobacteria were isolated from the sediment but they were present in both samples according to metabarcoding and their high abundance (49.3%) in the tubercle could indicate an important functional role. Although some sediment isolates and operational taxonomic units from the metabarcoding have previously been associated with surface colonisation or biofilm formation in MIC, there was no strong evidence for the notion that the sediment adjacent to ALWC was the source of tubercle microbes. Further isolation strategies and functional investigations of representative bacteria at different stages of corrosion are being carried out for additional laboratory-based corrosion studies.

Evidence for H2 consumption by uncultured Desulfobacterales in coastal sediments.

Molecular hydrogen (H2 ) is the key intermediate in the anaerobic degradation of organic matter. Its removal by H2 -oxidizing microorganisms is essential to keep anaerobic degradation energetically favourable. Sulfate-reducing microorganisms (SRM) are known as the main H2 scavengers in anoxic marine sediments. Although the community of marine SRM has been extensively studied, those consuming H2 in situ are completely unknown. We combined metagenomics, PCR-based clone libraries, single-amplified genomes (SAGs) and metatranscriptomics to identify potentially H2 -consuming SRM in anoxic coastal sediments. The vast majority of SRM-related H2 ase sequences were assigned to group 1b and 1c [NiFe]-H2 ases of the deltaproteobacterial order Desulfobacterales. Surprisingly, the same sequence types were similarly highly expressed in spring and summer, suggesting that these are stable and integral members of the H2 -consuming community. Notably, one sequence cluster from the SRM group 1 consistently accounted for around half of all [NiFe]-H2 ase transcripts. Using SAGs, we could link this cluster with the 16S rRNA genes of the uncultured Sva0081-group of the family Desulfobacteraceae. Sequencing of 16S rRNA gene amplicons and H2 ase gene libraries suggested consistently high in situ abundance of the Sva0081 group also in other marine sediments. Together with other Desulfobacterales these likely are important H2 -scavengers in marine sediments.

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.

Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads.

Pseudodesulfovibrio hydrargyri sp. nov., a mercury-methylating bacterium isolated from a brackish sediment.

The strain BerOc1T was isolated from brackish sediments contaminated with hydrocarbons and heavy metals. This strain has been used as a model strain of sulfate-reducer to study the biomethylation of mercury. The cells are vibrio-shaped, motile and not sporulated. Phylogeny and physiological traits placed this strain within the genus Pseudodesulfovibrio. Optimal growth was obtained at 30 °C, 1.5 % NaCl and pH 6.0-7.4. The estimated G+C content of the genomic DNA was 62.6 mol%. BerOc1T used lactate, pyruvate, fumarate, ethanol and hydrogen. Terminal electron acceptors used were sulfate, sulfite, thiosulfate and DMSO. Only pyruvate could be used without a terminal electron acceptor. The major fatty acids were C18 : 0, anteiso-C15 : 0, C16 : 0 and C18 : 1ω7. The name Pseudodesulfovibrio hydrargyri sp. nov. is proposed for the type strain BerOc1T (DSM 10384T=JCM 31820T).

Association of magnetotactic multicellular prokaryotes with Pseudoalteromonas species in a natural lagoon environment.

Magnetotactic bacteria, for the most part, are free-living, motile, unicellular prokaryotes that inhabit almost all marine and freshwater environments. One notable exception to the unicellular mode, however, are the magnetotactic multicellular prokaryotes. These morphologically unique prokaryotes (e.g., Candidatus Magnetoglobus multicellularis) are motile aggregates of 20-40 genetically identical, Gram-negative cells organised as a sphere (or ovoid in shape) and only motile as a unit. No specific close physical association between magnetotactic bacteria and non-magnetotactic microorganisms has ever been reported. Here, using culture-independent approaches, we show an unusual association between the spherical magnetotactic multicellular prokaryote Ca. Magnetoglobus multicellularis and Pseudoalteromonas species in environmental sediment and water samples collected from the Araruama Lagoon in Brazil. Cells of Pseudoalteromonas species were observed to be physically attached to the surface and, notably, even in the intercellular space of these spherical magnetotactic multicellular prokaryotes. An attempt to correlate the frequency of association between Pseudoalteromonas and magnetotactic multicellular prokaryotes with sediment depth was made but only a slight decrease in the number of Pseudoalteromonas cells per magnetotactic multicellular prokaryote was observed with increasing depth. Similar observations were made with magnetotactic multicellular prokaryotes from another Brazilian Lagoon (Rodrigo de Freitas) and the putative symbiont/parasite was detected. Although our results suggest some sort of specificity in the relationship between these prokaryotes, the precise nature of this association remains unclear.

Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales.

The unusual chemo-organoheterotrophic proteobacterial strain MWH-Nonnen-W8redT was isolated from a lake located in the Black Forest (Schwarzwald), Germany, by using the filtration-acclimatization method. Phylogenetic analyses based on the 16S rRNA gene sequence of the strain could not provide clear hints on classification of the strain in one of the current classes of the phylum Proteobacteria. Whole-genome sequencing resulted in a genome size of 3.5 Mbp and revealed a quite low DNA G+C content of 32.6 mol%. In-depth phylogenetic analyses based on alignments of 74 protein sequences of a phylogenetically broad range of taxa suggested assignment of the strain to a new order of the class Oligoflexia. These analyses also suggested that the order Bdellovibrionales should be transferred from the class Deltaproteobacteria to the class Oligoflexia, that this order should be split into two orders, and that the family Pseudobacteriovoracaceae should be transferred from the order Bdellovibrionales to the order Oligoflexales. We propose to establish for strain MWH-Nonnen-W8redT (=DSM 23856T=CCUG 58639T) the novel species and genus Silvanigrella aquatica gen. nov., sp. nov. to be placed in the new family Silvanigrellaceae fam. nov. of the new order Silvanigrellales ord. nov.

Desulfosarcina widdelii sp. nov. and Desulfosarcina alkanivorans sp. nov., hydrocarbon-degrading sulfate-reducing bacteria isolated from marine sediment and emended description of the genus Desulfosarcina.

In previous studies, two hydrocarbon-degrading sulfate-reducing bacteria, strains PP31T and PL12T, were obtained from oil-polluted marine sediments of Shuaiba, Kuwait. They had been reported as organisms capable of anaerobic degradation of p-xylene and n-alkanes, respectively. The 16S rRNA gene sequence of strain PP31T showed 98.8 % sequence similarities to that of Desulfosarcina variabilis'Montpellier'T. Strains PL12T had 97.8 % of sequence similarity to Desulfosarcina ovata oXys1T. They both have been partially characterized, but not been validly published as new species of the genus Desulfosarcina. In this study, additional characterizations of these strains were made to describe them as two new species of the genus Desulfosarcina. Major cellular fatty acids of strain PP31T were C15 : 0 (25.9 %) and anteiso-C15 : 0 (22.3 %), whereas those of strain PL12T were C15 : 0 (21.3 %), C16 : 0 (17.8 %) and anteiso-15 : 0 (11.6 %). The phylogenetic tree based on 16S rRNA gene revealed that these isolates should not be classified as any of the known species in the genus Desulfosarcina. On the basis of phenotypic and phylogenetic analyses, these two sulfate reducers are proposed to form two novel species of the genus Desulfosarcina : Desulfosarcina widdelii sp. nov. (PP31T=JCM 31729T=DSM 103921T) and Desulfosarcina alkanivorans sp. nov. (PL12T=JCM 31728T=DSM 103901T). In addition, emended description of the genus Desulfosarcina is presented in this study.

Desulfonatronum parangueonense sp. nov., a sulfate-reducing bacterium isolated from sediment of an alkaline crater lake.

Novel Gram-stain-negative, non-spore-forming, vibrio-shaped, anaerobic, alkaliphilic, sulfate-reducing bacteria, designated strains PAR180T and PAR190, were isolated from sediments collected at an alkaline crater lake in Guanajuato (Mexico). Strain PAR180T grew at temperatures between 15 and 40 °C (optimum 35 °C), and at pH between 8.3 and 10.4 (optimum 9). It was halotolerant, growing with up to 8 % (w/v) NaCl. Lactate, formate, pyruvate and ethanol were used as electron donors in the presence of sulfate and were incompletely oxidized to acetate and CO2. The isolate was able to grow with hydrogen and with CO2 as a carbon source. Beside sulfate, sulfite and thiosulfate were used as terminal electron acceptors. The isolate was able to grow by disproportionation of sulfite and thiosulfate, but not elemental sulfur, using acetate as a carbon source. The predominant fatty acids were C16 : 0, C16 : 1ω7c and summed feature 10 (C18 : 1ω7c and/or C18 : 1ω9t and/or C18 : 1ω12t). The DNA G+C content was 56.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that it belongs to the genus Desulfonatronum, class Deltaproteobacteria. Its closest relative is Desulfonatronum thiosulfatophilum (98.7 % 16S rRNA gene sequence similarity). The DNA-DNA relatedness value between strain PAR180T and the type strain of D. thiosulfatophilum was 37.1±2.5 %. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, the isolates is considered to represent a novel species of the genus Desulfonatronum, for which the name Desulfonatronum parangueonense sp. nov. is proposed. The type strain is PAR180T (=DSM 103602T=JCM 31598T).

Desulfobulbus oligotrophicus sp. nov., a sulfate-reducing and propionate-oxidizing bacterium isolated from a municipal anaerobic sewage sludge digester.

A novel, mesophilic, strictly anaerobic, sulfate-reducing and propionate-oxidizing bacterium, strain Prop6T, was enriched and isolated from a municipal anaerobic sewage sludge digester. Cells were Gram-stain-negative, catalase-positive, oval rods, motile by means of amphitrichous flagella, non-spore-forming and contained menaquinone MK-5(H2) as the major respiratory quinone. The genomic DNA G+C content was 51.7 mol%. The optimal NaCl concentration, temperature and pH were 2-5 g l-1, 35 °C and pH 7.6, respectively. Strain Prop6T could only oxidize propionate, lactate and pyruvate (weakly) with sulfate, sulfite or thiosulfate, mainly to acetate. Strain Prop6T fermented pyruvate and lactate to acetate and propionate. The predominant cellular fatty acids were C14 : 0, C16 : 0, C16 : 1ω7, C16 : 1ω5, C17 : 1ω6 and C18 : 1ω7. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genus Desulfobulbus, with Desulfobulbus elongatus DSM 2908T, Desulfobulbus propionicus DSM 2032T and Desulfobulbus rhabdoformis DSM 8777T as closest relatives among species with validly published names. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Desulfobulbus oligotrophicus sp. nov. The type strain is Prop6T (=DSM 103420T=JCM 31535T).

Desulfonatronospira sulfatiphila sp. nov., and Desulfitispora elongata sp. nov., two novel haloalkaliphilic sulfidogenic bacteria from soda lakes.

Two novel haloalkaliphilic bacteria with dissimilatory sulfidogenic metabolism were recovered from syntrophic associations obtained from anaerobic sediments of hypersaline soda lakes in Kulunda Steppe (Altai, Russia). Strain ASO3-2T was a member of a sulfidogenic syntrophic association oxidizing acetate at extremely haloalkaline conditions, and was isolated in pure culture using formate as electron donor and sulfate as electron acceptor. It was identified as representing a novel member of the genus Desulfonatronospira within the Deltaproteobacteria. In contrast to the two known species of this genus, the novel isolate was able to grow with formate as electron donor and sulfate, as well as with sulfite, as electron acceptor. Strain Acr1T was a minor component in a soda lake syntrophic association converting benzoate to methane and acetate. It became dominant in a subculture fed with crotonate. While growing on crotonate, strain Acr1T formed unusually long cells filled with polyhydroxyalkanoate-like granules. Its metabolism was limited to fermentation of crotonate and pyruvate and the ability to utilize thiosulfate and sulfur/polysulfide as electron acceptor. Strain Acr1T was identified as representing a novel member of the genus Desulfitispora in the class Clostridia. Both isolates were obligately haloalkaliphilic with extreme salt tolerance. On the basis of phenotypic and phylogenetic analyses, the novel sulfidogenic isolates from soda lakes are proposed to represent two novel species: Desulfonatronospira sulfatiphila sp. nov. (ASO3-2T=DSM 100427=UNIQEM U993T) and Desulfitispora elongata sp. nov. (Acr1T=DSM 29990=UNIQEM U994T).

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle.

During the last decades, our knowledge about the activity of sponge-associated microorganisms and their contribution to biogeochemical cycling has gradually increased. Functional groups involved in carbon and nitrogen metabolism are well documented, whereas knowledge about microorganisms involved in the sulfur cycle is still limited. Both sulfate reduction and sulfide oxidation has been detected in the cold water sponge Geodia barretti from Korsfjord in Norway, and with specimens from this site, the present study aims to identify extant versus active sponge-associated microbiota with focus on sulfur metabolism. Comparative analysis of small subunit ribosomal RNA (16S rRNA) gene (DNA) and transcript (complementary DNA (cDNA)) libraries revealed profound differences. The transcript library was predominated by Chloroflexi despite their low abundance in the gene library. An opposite result was found for Acidobacteria. Proteobacteria were detected in both libraries with representatives of the Alpha- and Gammaproteobacteria related to clades with presumably thiotrophic bacteria from sponges and other marine invertebrates. Sequences that clustered with sponge-associated Deltaproteobacteria were remotely related to cultivated sulfate-reducing bacteria. The microbes involved in sulfur cycling were identified by the functional gene aprA (adenosine-5'-phosphosulfate reductase) and its transcript. Of the aprA sequences (DNA and cDNA), 87 % affiliated with sulfur-oxidizing bacteria. They clustered with Alphaproteobacteria and with clades of deep-branching Gammaproteobacteria. The remaining sequences clustered with sulfate-reducing Archaea of the phylum Euryarchaeota. These results indicate an active role of yet uncharacterized Bacteria and Archaea in the sponge's sulfur cycle.

'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen.

Termite gut flagellates are typically colonized by specific bacterial symbionts. Here we describe the phylogeny, ultrastructure and subcellular location of 'Candidatus Adiutrix intracellularis', an intracellular symbiont of Trichonympha collaris in the termite Zootermopsis nevadensis. It represents a novel, deep-branching clade of uncultured Deltaproteobacteria widely distributed in intestinal tracts of termites and cockroaches. Fluorescence in situ hybridization and transmission electron microscopy localized the endosymbiont near hydrogenosomes in the posterior part and near the ectosymbiont 'Candidatus Desulfovibrio trichonymphae' in the anterior part of the host cell. The draft genome of 'Ca. Adiutrix intracellularis' obtained from a metagenomic library revealed the presence of a complete gene set encoding the Wood-Ljungdahl pathway, including two homologs of fdhF encoding hydrogenase-linked formate dehydrogenases (FDHH ) and all other components of the recently described hydrogen-dependent carbon dioxide reductase (HDCR) complex, which substantiates previous claims that the symbiont is capable of reductive acetogenesis from CO2 and H2 . The close phylogenetic relationship between the HDCR components and their homologs in homoacetogenic Firmicutes and Spirochaetes suggests that the deltaproteobacterium acquired the capacity for homoacetogenesis via lateral gene transfer. The presence of genes for nitrogen fixation and the biosynthesis of amino acids and cofactors indicate the nutritional nature of the symbiosis.